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<h3> Data </h3>

<h4> Loading data </h4>

<p>
Seed requires input data in a specific format. The data should be in two separate files, one for metadata and the other for abundance data. Seed accepts .csv (comma delimited) formated files by default, but other delimiting characters may be specified by clicking the 'Show file options' box.
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<p>
The metaData file should include sample information. Samples should be in rows, with sample names in the first column. Additional columns may include any information about the samples. The taxa file should include abundance data. Samples should be in rows, with sample names in the first column. Additional columns should list taxa abundance. The abundance may be presence/absence, relative abundance, or count data. Please see the Ravel et al. dataset for an example of input file formatting.
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<h4> Dataset verification </h4>

<p>
Seed provides a number of features that may be used to verify that files have been loaded correctly. The first five samples for both the metadata file and the taxa file are displayed in the main window. Users should check that the data appears as expected.
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<p>
Seed automatically associates sample information with abundance measurements using the sample names. Samples that are not present in both the metadata file and the taxa file are discarded. Seed generates a Venn diagram showing how many samples were detected in each file, and how many samples the files shared.
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<h4> Diversity indices </h4>

<p>

After loading the abundance data, Seed automatically calculates several diversity indices and adds them to the sample information. These diversity calculations include the Shannon, Simpson, and Inverse Simpson indices. They are calculated using the vegan R package and may not be appropriate for every type of data. If these indices are used, the user should make sure that they are appropriate for the abundance data being analyzed.
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<h4> Abundance data transformations </h4>

<p>
Seed includes options for relative abundance, presence/absence, and Hellinger data transformations. Relative abundance is calculated by dividing each taxa count by the sum of all taxa counts for each sample. Presence/absence converts every non-zero taxa to 1. The converted data is used for all visualizations and summaries.
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<h4> Advanced options </h4>

<p>
Seed supports saving plots in two different file formats. The user may select either PDF or PNG formats. All saved plots will be in the format selected in the 'Data' tab.
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<h4> Important functions </h4>

<p>
gplots::venn - generates Venn diagram
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<p>
vegan::decostand - transforms data
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vegan::diversity - calculates diversity indices
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<h5>Citation for package vegan</h5>

<blockquote>
Jari Oksanen, F. Guillaume Blanchet, Roeland Kindt, Pierre Legendre, Peter R. Minchin, R. B. O'Hara, Gavin L. Simpson, Peter Solymos, M. Henry H. Stevens and Helene Wagner (2013). vegan: Community Ecology Package. R package version 2.0-10. http://CRAN.R-project.org/package=vegan
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<h5>Citation for package gplots</h5>
<blockquote>
Gregory R. Warnes, Ben Bolker, Lodewijk Bonebakker, Robert Gentleman, Wolfgang Huber Andy Liaw, Thomas Lumley, Martin Maechler, Arni Magnusson, Steffen Moeller, Marc Schwartz and Bill Venables (2013). gplots: Various R programming tools for plotting data. R package version 2.12.1. http://CRAN.R-project.org/package=gplots
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